Cilia are cellular organelles that are essential for human development and health. It has long been known that cilia are organized into structurally and functionally distinct compartments known as the basal body, the transition zone, and the cilia shaft. Nephronophthisis-related ciliopathy (NPHP-RC) proteins localize to subregions within the previously known compartments, revealing a hidden structural complexity. For example, NPHP2/Inversin localizes to a proximal region of the ciliary shaft called the Inversin Compartment (InvC) that is not identifiable by any ultrastructural features. Despite the profound medical importance of cilia in human health and disease, how this region of the cilium is spatially and functionally organized remains poorly understood. Identifying mechanisms controlling cilia shaft compartmentalization and understanding the physiological relevance of ciliary territories will be important in identifying therapeutic targets to combat cystic kidney diseases and other ciliopathies associated with ciliary defects. The InvC is conserved in the nematode C. elegans, suggesting that the logic underlying the establishment of the InvC and ciliary compartmentalization is similar in worm and human cilia. In C. elegans, we found that the InvC and microtubule (MT) doublet region genes function in modules to regulate ciliogenesis, MT patterning, and tubulin glutamylation. nphp-2 genetically interacts with the transition zone NPHP-RC modules, indicating inter-compartmental crosstalk between the InvC and transition zone components. In this competing renewal application, we use C. elegans, an exceptional model for ciliary biology and human ciliopathies, to address the question of how the cilium is spatially and functional organized. First, we will define the origin and function of the Inversin compartment. To this end, we will study InvC temporal and spatial regulation; ascertain how the InvC is established and determine whether tubulin glutamylation plays a role; and determine how the deacetylase HDAC-6 antagonizes InvC- and MT doublet region component-mediated ciliogenesis. Second, we determine how ciliary stability regulated by tubulin polyglutamylation may be involved in NPHP-RCs. We will test the hypothesis that NPHP- RC transition zone, InvC, and doublet region components regulate ciliary access and localization of tubulin glutamylases and deglutamylases. We will determine how tubulin polyglutamylation regulates ciliary motor- based transport and MT ultrastructure. We will identify suppressors of ciliary degeneration in the tubulin deglutamylase mutant ccpp-1. This research will address the medically relevant question of how cilia are structurally and functionally organized in healthy and diseased states, and will provide fundamental insight to the molecules, mechanisms, and functions of ciliary compartmentalization and tubulin post-translational modifications. These studies have direct implications for cystic kidney disease research because many of the genes and pathways explored in our work are associated with ciliopathies.